Human rhinovirus (HRV) infection causes at least 50% of asthma exacerbations. Airway epithelial cell (AEC) infection evokes the release of inflammatory, growth and bronchospastic factors, and other autocrine/paracrine mediators leading to generalized AEC and airway smooth muscle (ASM) pro-exacerbation pathology. This includes altered AEC lining fluid/ion content, ASM hyperreactivity, and ASM resistance to relaxation by (-agonists, which are controlled by G-protein coupled receptors (GPCRs) on these cells. The heterogeneity of these asthmatic responses is, in part, thought to be dependent on the HRV strain (serotype). There are over 100 HRV strains, yet little is known about how genomic differences in strains impact asthma exacerbation phenotypes. We have very recently completed sequencing the genomes of all 99 reference HRV-A and -B serotypes from a banked historical repository. This revealed previously unknown aspects of HRV RNA and protein structure, phylogenetic relationships, recombination, and extensive diversity among the canonical serotypes. It also provided structure-based sequence alignments which are a scaffold for integration of additional HRVs into the phylogenetic tree. The broad long-term objectives of this revised proposal are to ascertain the genomic features of modern HRV strains that contribute to specific asthmatic airway GPCR phenotypes and their heterogeneity. This will be accomplished by three aims. In Aim 1, we will determine the complete genome sequences of HRVs from 200 modern clinical isolates using massively parallel sequencing methods. In Aim 2, this data will be integrated into our structure-based reference genomic scaffold so as to define genomic regions that are similar and dissimilar amongst the strains, providing a rigorous mechanism to select the HRVs for in vitro functional studies. In Aim 3, GPCR signaling phenotypes of HRVs in the context of AEC and ASM will be ascertained in cell culture models using high-throughput methods (Sub Aim 1). And, these signaling phenotypes will be correlated to HRV genome features using Bayesian techniques with internal and external validations (Sub Aim 2). Such studies will provide a genomic basis for those HRVs that do, and do not, evoke AEC and ASM phenotypic traits, and thus establish some of the mechanisms of heterogeneity of viral induced asthma exacerbations. These findings may provide diagnostic and prognostic information, and pharmacologic strategies, for managing the most common cause of asthma exacerbations. PUBLIC HEALTH RELEVANCE: Human rhinovirus (HRV) infection causes about 50% of asthma attacks (and COPD exacerbations). There is, though, substantial variability in the nature and severity of the clinical features of asthma attacks from HRV infections, for reasons that are not known. However, it is now clear that there are many distinct HRV strains, and this proposal will define which HRVs, and which parts of their genomes, impose changes in airway receptor function that contribute to the pathology and symptoms of asthmatic attacks during HRV infection.